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Structure of protein kinase C theta with compound 10: 2,2-dimethyl-7- (2-oxidanylidene-3~{H}-IMIDAZO[4,5-B]PYRIDIN-1-yl)-1-(phenylmethyl)- 3~{H}-quinazolin-4-one

Analyse Structure of protein kinase C theta with compound 10: 2,2-dimethyl-7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F9E
Type: protein
Length: 630 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein kinase C theta type
EC: 2.7.11.13
UniProt: Q04759
Ligands: 5VS
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein kinase C theta type (EC 2.7.11.13)	protein	336	40% helix, 17% strand	Q04759
B	Protein kinase C theta type (EC 2.7.11.13)	protein	294	38% helix, 18% strand	Q04759

Ligands and binding sites

5VS · 2,2-dimethyl-7-(2-oxidanylidene-3~{H}-imidazo[4,5-b]pyridin-1-yl)-1-(phenylmethyl)-3~{H}-quinazolin-4-one · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.78	0.83	54	5VS
2	517	0.69	0.79	56	5VS
3	193	0.53	0.78	33	empty
4	82	0.31	0.73	17	empty
5	64	0.30	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 728 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (phosphorylation).

Compared structures

5F9E · Structure of Protein Kinase C theta with compound 10… · the same entry in another collection · chain A against A, TM-score 1.00
Q04759 · AlphaFold monomer V2.0 prediction for protein kinase C theta type (Q04759) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q04759
Elsewhere: RCSB PDB 5F9E · PDBe 5F9E · UniProt Q04759

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